United States

Molecular representation learning is a fundamental problem in the field of drug discovery and molecular science. Whereas incorporating molecular 3D information in the representations of molecule seems beneficial, which is related to computational chemistry with the basic task of predicting stable 3D structures (conformations) of molecules. Existing machine learning methods either rely on 1D and 2D molecular properties or simulate molecular force field to use additional 3D structure information via Hamiltonian network. The former has the disadvantage of ignoring important 3D structure features, while the latter has the disadvantage that existing Hamiltonian neural network must satisfy the “canonial” constraint, which is difficult to be obeyed in many cases. In this paper, we propose a novel plug-and-play architecture LagNet by simulating molecular force field only with parameterized position coordinates, which implements Lagrangian mechanics to learn molecular representation by preserving 3D conformation without obeying any additional restrictions. LagNet is designed to generate known conformations and generalize for unknown ones from molecular SMILES. Implicit positions in LagNet are learned iteratively using discrete-time Lagrangian equations. Experimental results show that LagNet can well learn 3D molecular structure features, and outperforms previous state-of-the-art baselines related molecular representation by a significant margin.

AAAI 2023

LagNet: Deep Lagrangian Mechanics for Plug-and-Play Molecular Representation Learning

ml: representation learning

app: bioinformatics

ml: deep neural network algorithms

The Human Glycome Project (HGP) is led by a consortium of research groups that shares a common goal of aiming to define the structures and functions of human glycoconjugates.


The 3rd Meeting of the Human Glycome Project

poster

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. AAAI-23 is the Thirty-Seventh AAAI Conference on Artificial Intelligence. The theme of this conference is to create collaborative bridges within and beyond AI. Like previous AAAI conferences, AAAI-23 will feature technical paper presentations, special tracks, invited speakers, workshops, tutorials, poster sessions, senior member presentations, competitions, and exhibit programs, and two new activities: a Bridge Program and a Lab Program. Many of these activities are tailored to the theme of bridges and all are selected according to the highest standards, with additional programs for students and young researchers. 
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The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines.

Hashing has been widely researched to solve the large-scale approximate nearest neighbor search problem owing to its time and storage superiority. In recent years, a number of online hashing methods have emerged, which can update the hash functions to adapt to the new stream data and realize dynamic  retrieval. However, existing online hashing methods are required to update the whole database with the latest hash functions when a query arrives, which leads to low retrieval efficiency with the continuous increase of the stream data. On the other hand, these methods ignore the supervision relationship among the examples, especially in the multi-label case. In this paper, we propose a novel Fast Online Hashing (FOH) method which only updates the binary codes of a small part of the database. To be specific, we first build a query pool in which the nearest neighbors of each central point are recorded. When a new query arrives, only the binary codes of the corresponding potential neighbors are updated. In addition, we create a similarity matrix which takes the multi-label supervision information into account and bring in the multi-label projection loss to further preserve the similarity among the multi-label data. The experimental results on two common benchmarks show that the proposed FOH can achieve dramatic superiority on query time up to 6.28 seconds less than state-of-the-art baselines with competitive retrieval accuracy.

Fast Online Hashing with Multi-Label Projection

Active Learning is an essential method for label-efficient deep learning. As a Bayesian active learning method, Bayesian Active Learning by Disagreement (BALD) successfully selects the most representative samples by maximizing the mutual information between the model prediction and model parameters. However, when applied to a batch acquisition mode, like batch construction with greedy search, BALD suffers from poor performance, especially with noises of near-duplicate data. To address this shortcoming, we propose a diverse beam search optimized batch active learning method, which explores a graph for every batch construction by expanding the highest-scored samples of a predetermined number. To avoid near duplicate beam branches (very similar beams generated from the same root and similar samples), which is undesirable for lacking diverse representations in the feature space, we design a self-adapted constraint within candidate beams. The proposed method is able to acquire data that can better represent the distribution of the unlabeled pool, and at the same time, be significantly different from existing beams. We observe that the proposed method achieves higher batch performance than the baseline methods on three benchmark datasets.

Beam Search Optimized Batch Bayesian Active Learning

Pretrained code language models have enabled great progress towards program synthesis. However, common approaches only consider in-file local context and thus miss information and constraints imposed by other parts of the codebase and its external dependencies. Existing code completion benchmarks also lack such context. To resolve these restrictions we curate a new dataset of permissively licensed Python packages that includes full projects and their dependencies and provide tools to extract non-local information with the help of program analyzers. We then focus on the task of function call argument completion which requires predicting the arguments to function calls. We show that existing code completion models do not yield good results on our completion task. To better solve this task, we query a program analyzer for information relevant to a given function call, and consider ways to provide the analyzer results to different code completion models during inference and training. Our experiments show that providing access to the function implementation and function usages greatly improves the argument completion performance. Our ablation study provides further insights on how different types of information available from the program analyzer and different ways of incorporating the information affect the model performance.

Better Context Makes Better Code Language Models: A Case Study on Function Call Argument Completion

In shilling attacks, an adversarial party injects a few fake user profiles into a Recommender System (RS) so that the target item can be promoted or demoted. Although much effort has been devoted to developing shilling attack methods, we find that existing approaches are still far from practical. In this paper, we analyze the properties a practical shilling attack method should have and propose a new concept of Cross-system Attack. With the idea of Cross-system Attack, we design a Practical Cross-system Shilling Attack (PC-Attack) framework that requires little information about the victim RS model and the target RS data for conducting attacks. PC-Attack is trained to capture graph topology knowledge from public RS data in a self-supervised manner. Then, it is fine-tuned on a small portion of target data that is easy to access to construct fake profiles. Extensive experiments have demonstrated the superiority of PC-Attack over state-of-the-art baselines. Our implementation of PC-Attack is available at https://github.com/KDEGroup/PC-Attack.

Practical Cross-system Shilling Attacks with Limited Access to Data

The conditional commitment abilities of mutually transparent computer agents have been studied in previous work on commitment games and program equilibrium. This literature has shown how these abilities can help resolve Prisoner’s Dilemmas and other failures of cooperation in complete information settings. But inefficiencies due to private information have been neglected thus far in this literature, despite the fact that these problems are pervasive and might also be addressed by greater mutual transparency. In this work, we introduce a framework for commitment games with a new kind of conditional commitment device, which agents can use to conditionally disclose private information. We prove a folk theorem for this setting that provides sufficient conditions for ex post efficiency, and thus represents a model of ideal cooperation between agents without a third-party mediator. Further, extending previous work on program equilibrium, we develop an implementation of conditional information disclosure. We show that this implementation forms program ε-Bayesian Nash equilibria corresponding to the Bayesian Nash equilibria of these commitment games.

Commitment Games with Conditional Information Disclosure

Zero-shot learning (ZSL) aims to predict unseen classes whose samples have never appeared during training. One of the most effective and widely used semantic information for zero-shot image classification are attributes which are annotations for class-level visual characteristics. However, the current methods often fail to discriminate those subtle visual distinctions between images due to not only the shortage of fine-grained annotations, but also the attribute imbalance and co-occurrence.  In this paper, we present a transformer-based end-to-end ZSL method named DUET, which integrates latent semantic knowledge from the pre-trained language models (PLMs) via a self-supervised multi-modal learning paradigm. Specifically, we (1) developed a cross-modal semantic grounding network to  investigate the model's capability of disentangling semantic attributes from the images; (2) applied an attribute-level contrastive learning strategy to further enhance the model's discrimination on fine-grained visual characteristics against the attribute co-occurrence and imbalance; (3) proposed a multi-task learning policy for considering multi-model objectives. We find that our DUET can achieve state-of-the-art performance on three standard ZSL benchmarks and a knowledge graph equipped ZSL benchmark. Its components are effective and its predictions are interpretable.

DUET: Cross-modal Semantic Grounding for Contrastive Zero-shot Learning

Parallel tempering (PT), also known as replica exchange, is the go-to workhorse for simulations of multi-modal distributions. The key to the success of PT is to adopt efficient swap schemes. The popular deterministic even-odd (DEO) scheme exploits the non-reversibility property and has successfully reduced the communication cost from $O(P^2)$ to $O(P)$ given sufficiently many $P$ chains. However, such an innovation largely disappears in big data due to the limited chains and few bias-corrected swaps. To handle this issue, we generalize the DEO scheme to promote non-reversibility and propose a few solutions to tackle the underlying bias caused by the geometric stopping time. Notably, in big data scenarios, we obtain an appealing communication cost $O(P\log P)$ based on the optimal window size. In addition, we also adopt stochastic gradient descent (SGD) with large and constant learning rates as exploration kernels. Such a user-friendly nature enables us to conduct approximation tasks for complex posteriors without much tuning costs.

Non-reversible Parallel Tempering for Deep Posterior Approximation

Dependency stochastic Boolean satisfiability (DSSAT) generalizes stochastic Boolean satisfiability (SSAT) in existential variables being Henkinized allowing their dependencies on randomized variables to be explicitly specified. It allows NEXPTIME problems of reasoning under uncertainty and partial information to be compactly encoded. To date, no decision procedure has been implemented for solving DSSAT formulas. This work provides the first such tool by converting DSSAT into SSAT with dependency elimination, similar to converting dependency quantified Boolean formula (DQBF) to quantified Boolean formula (QBF). Moreover, we extend (D)QBF preprocessing techniques and implement the first standalone (D)SSAT preprocessor. Experimental results show that solving DSSAT via dependency elimination is highly applicable and that existing SSAT solvers may benefit from preprocessing.

Lifting (D)QBF Preprocessing and Solving Techniques to (D)SSAT

We present HetNet (Multi-level \textbf{Het}erogeneous \textbf{Net}work), a highly efficient mirror detection network. Current mirror detection methods focus more on performance than efficiency, limiting the real-time applications (such as drones). Their lack of efficiency is aroused by the common design of adopting homogeneous modules at different levels, which ignores the difference between different levels of features. In contrast, HetNet detects potential mirror regions initially through low-level understandings (\textit{e.g.}, intensity contrasts) and then combines with high-level understandings (contextual discontinuity for instance) to finalize the predictions. To perform accurate yet efficient mirror detection, HetNet follows an effective architecture that obtains specific information at different stages to detect mirrors. We further propose a multi-orientation intensity-based contrasted module (MIC) and a reflection semantic logical module (RSL), equipped on HetNet, to predict potential mirror regions by low-level understandings and analyze semantic logic in scenarios by high-level understandings, respectively. Compared to the state-of-the-art method, HetNet runs 664% faster and draws an average performance gain of 8.9% on MAE, 3.1% on IoU, and 2.0% on F-measure on two mirror detection benchmarks.

Efficient Mirror Detection via Multi-level Heterogeneous Learning

Modeling continuous dynamical systems from discretely sampled observations is a fundamental problem in data science. Often, such dynamics are the result of non-local processes that present an integral over time. As such, these systems are modeled with Integro-Differential Equations (IDEs); generalizations of differential equations that comprise both an integral and a differential component. For example, brain dynamics are not accurately modeled by differential equations since their behavior is non-Markovian, i.e. dynamics are in part dictated by history. Here, we introduce the Neural IDE (NIDE), a novel deep learning framework based on the theory of IDEs where integral operators are learned using neural networks.  
    We test NIDE on several toy and brain activity datasets and demonstrate that NIDE outperforms other models. These tasks include time extrapolation as well as predicting dynamics from unseen initial conditions, which we test on whole-cortex activity recordings in freely behaving mice. Further, we show that NIDE can decompose dynamics into their Markovian and non-Markovian constituents, via the learned integral operator, which we test on fMRI brain activity recordings of people on ketamine. Finally, the integrand of the integral operator provides a latent space that gives insight into the underlying dynamics, which we demonstrate on wide-field brain imaging recordings. Altogether, NIDE is a novel approach that enables modeling of complex non-local dynamics with neural networks.

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Fast Online Hashing with Multi-Label Projection

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